The ATP-dependent chromatin-remodeling complexes play important roles in gene regulation by opening chromatin structures for transcriptional activators or repressors. The prototype of this type of complexes is the SWI/SNF complex, which was found in diverse organisms, including yeast, Drosophila, mouse and human. It is required for proper expression of homeotic genes and segmentation in Drosophila, and mutation in one subunit of the complex causes pediatric rhabdoid cancer in humans. We have purified several human SWI/SNF-related complexes. By microsequencing, we have identified and cloned all the subunits from the major form of the complex. Analysis revealed that BAF250a contains a DNA binding domain similar to yeast SWI1, and several LXXLL motifs, which have been previously shown to be able to interact with nuclear hormone receptors. Using transient transfection assays, we found that BAF250a in fact facilitates transcriptional activation by glucocorticoid receptor (GR). The region containing LXXLL motifs of BAF250 also interacts with GR in vitro. This work suggests that BAF250a may be a targeting subunit of hSWI/SNF, and may mediate the recruitment of the complex to DNA-bound glucocorticoid receptors. As a continuation of this project, we have cloned a novel human homolog of BAF250a, termed BAF250b. The two genes share over 60% of identity and possess same type of domain structure. We have now isolated a BAF250b-containing complex. It shares several identical subunits with BAF250a complex but also contains its own unique components. One unique subunit is ENL, a fusion partner for MLL which is a common target for chromosomal translocation in human acute leukemia. ENL is also the human ortholog of yeast SWI/SNF subunit, TFG3. We demonstrated that the resultant MLL-ENL fusion protein also assciates with a human SWI/SNF complex. Moreover, the fusion protein cooperates with SWI/SNF to activate the promoter of HOXA7, which is a downstream target of MLL and is essential for oncogenic activity of the MLL fusion proteins. Our data suggest that human SWI/SNF complexes show considerable hetergeneity, and one or more may be involved in the etiology of leukemia by functioning with MLL-fusion proteins. We are continuing to identify the genes that are specifically dependent on BAF, but not PBAF, for expression. Using siRNA, we were able to deplete the BAF-specific subunit, BAF250. We showed that one interferon-responsive gene, IFGM3, specifically depends on BAF but not PBAF for expression. This result demonstrates that BAF and PBAF have selectivity in mediating expression of different genes. We plan to investigate the mechanism of how BAF is targeted to IFGM3 and other genes. Recently, we initiated a new collaborative project with Drs. Minoru Ko and Zhong Wangs labs to study the function of SWI/SNF complexes in the maintenance of pluripotency of ES cells. SWI/SNF chromatin remodeling complexes are known to be essential for early embryonic development in mice. However, the roles of these complexes in embryonic stem (ES) cells are poorly understood. One reason is that mice deficient in common components of SWI/SNF complexes die very early, before the ES cells can be established. In this project, we show that two subgroups of SWI/SNF complexes associated with BAF250a (a.k.a. Arid1a) and BAF250b (a.k.a. Arid1b) are present at high levels in undifferentiated ES cells, and their levels decrease when ES cells are induced to differentiate. We generated mouse ES cells deficient in BAF250b by gene targeting, and found that these cells have a reduced proliferation rate and an abnormal cell cycle. More importantly, they lost the self-renewal capacity of ES cells and displayed multiple markers characteristic of differentiated cells. Microarray and subsequent qRT-PCR analysis confirmed that these cells have reduced expression of several genes involved in pluripotency of ES cells, and increased expression of several differentiation genes. These data suggest that the BAF250b-associated SWI/SNF is essential for mouse ES cells to maintain its normal proliferation and undifferentiated state. On a related project, we collaborated with Drs. Gong and Smerdon's labs and showed that SWI/SNF complex is involved in the cellular response pathway to UV-induced DNA damage. This study uncovers another mechanism of SWI/SNF in protecting genome stability. We also studied the regulation of MeCP2, a methyl DNA binding protein involved in Rett syndrome. Rett syndrome is a neurological disorder and one of the most common causes of mental retardation in girls. In up to 80% of the patients, the defects lie in mutation of the MeCP2 gene. MeCP2 consists of a DNA binding domain specific for methylated CpG dinucleotide, and a transcriptional repression domain. It could therefore bind methylated DNA through its binding domain and then silence gene expression through its repression domain. Indeed, MeCP2 has been shown to function as a transcriptional repressor both in vivo and in vitro. One previous publication suggested that MeCP2 functions through its stable association with SWI/SNF chromatin remodeling complex. We immunopurified MeCP2 and SWI/SNF complex, and found that there is no detectable association between these molecules. A previous study has shown that MeCP2 becomes hyperphosphorylated at S421 when neurons are induced to undergo depolarization. This phosphorylation inhibits MeCP2 DNA-binding activity, which correlates with increased transcription of BDNF, an important regulator for neuronal function. We used mass spectrometry to identify 5 phosphorylation sites in MeCP2 purified from normal mouse brain, and 2 additional sites in MeCP2 from mice induced to undergo seizure. We have also successfully generated one phosphorylation site-specific antibody for Ser80, and were able to confirm phosphorylation at Ser80 in vivo. In collaboration with Dr. Y. Suns lab at UCLA, we find that although the total level of MeCP2 phosphorylation is increased during depolarization of neurons, the level of phosphorylation at Ser80 is actually decreased. Furthermore, we find that mutating Ser80 to alanine (S80A) reduces BDNF gene expression in cultured neurons derived from either normal mice or MeCP2-null mice. These data suggest an important role of phosphorylation at Ser80 in MeCP2 function. By chromatin-IP, we found that an S80A mutation increased the level of MeCP2 bound to the BDNF promoter in vivo, which correlates with the observation that the same mutation reduced BDNF transcription. Through collaboration with Drs. Qiang Chang and Rudy Jaenisch (MIT), a knock-in mutant that substitutes Ser80 with alanine has been generated in mice. These mice exhibit locomotor deficits, a phenotype observed in Rett syndrome patients. The data provide in vivo evidence for the functional significance of MeCP2 phosphorylation.